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- PDB-4g1u: X-ray structure of the bacterial heme transporter HmuUV from Yers... -

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Basic information

Entry
Database: PDB / ID: 4g1u
TitleX-ray structure of the bacterial heme transporter HmuUV from Yersinia pestis
Components
  • Hemin import ATP-binding protein HmuV
  • Hemin transport system permease protein hmuU
KeywordsTRANSPORT PROTEIN/HYDROLASE / membrane transporter / Type II ABC importer / HmuT / plasma membrane / TRANSPORT PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


ABC-type heme transporter activity / siderophore-dependent iron import into cell / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / plasma membrane => GO:0005886 / transmembrane transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
: / Hemin import ATP-Binding protein hmuV family profile. / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, BtuC-like / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...: / Hemin import ATP-Binding protein hmuV family profile. / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, BtuC-like / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Hemin transport system permease protein HmuU / Hemin import ATP-binding protein HmuV
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.008 Å
AuthorsWoo, J.-S. / Goetz, B.A. / Zeltina, A. / Locher, K.P.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: X-ray structure of the Yersinia pestis heme transporter HmuUV.
Authors: Woo, J.-S. / Zeltina, A. / Goetz, B.A. / Locher, K.P.
History
DepositionJul 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemin transport system permease protein hmuU
B: Hemin transport system permease protein hmuU
C: Hemin import ATP-binding protein HmuV
D: Hemin import ATP-binding protein HmuV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,2796
Polymers136,0894
Non-polymers1902
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-87 kcal/mol
Surface area45610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.870, 101.230, 105.210
Angle α, β, γ (deg.)90.000, 91.300, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN A AND NOT ((RESSEQ 27:28) OR (RESSEQ 48:49) OR (RESSEQ 51) OR (RESSEQ 55))A0
211CHAIN B AND NOT ((RESSEQ 27:28) OR (RESSEQ 48:49) OR (RESSEQ 51) OR (RESSEQ 55))B0
112CHAIN C AND NOT ((RESSEQ 1:9))C0
212CHAIN D AND NOT ((RESSEQ 1:9))D0
113CHAIN C AND (RESSEQ 301)C1 - 301
213CHAIN D AND (RESSEQ 301)D1 - 301

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Hemin transport system permease protein hmuU


Mass: 38356.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: hmuU, YPO0280, y0540, YP_0435 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56992
#2: Protein Hemin import ATP-binding protein HmuV


Mass: 29688.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: hmuV, YPO0279, y0539, YP_0434 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q56993, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.95 Å3/Da / Density % sol: 68.83 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 26, 2010
RadiationMonochromator: double-crystal fixed-exit / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionNumber: 177675 / Rmerge(I) obs: 0.111 / D res high: 3.48 Å / Num. obs: 52844 / % possible obs: 97.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
15.5829.7752785.410.054
11.0215.58109499.610.058
8.9911.02142399.910.054
7.798.99168198.610.061
6.977.79192699.110.073
6.366.97210099.210.094
5.896.3622749910.125
5.515.89248399.410.128
5.195.51269699.710.131
4.935.19273599.110.123
4.74.93294299.510.133
4.54.7304399.510.166
4.324.5321899.410.208
4.164.32331998.510.277
4.024.16335798.210.375
3.894.02351498.810.539
3.783.89362798.710.629
3.673.78381599.210.872
3.573.67392399.311.118
3.483.57314778.611.683
ReflectionResolution: 2.99→30 Å / Num. all: 42831 / Num. obs: 42310 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 93.481 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.99-3.071.8421.2810694315528011.29788.8
3.07-3.161.5281.812921307330661.02799.8
3.16-3.250.9912.6712476298629840.64399.9
3.25-3.350.7863.3911989289128870.52899.9
3.35-3.460.5834.5611511279727930.35599.9
3.46-3.580.4485.8611212275527470.26799.7
3.58-3.710.3587.2710336261226050.299.7
3.71-3.870.28699730252025110.14999.6
3.87-4.040.2459.958784245124440.12599.7
4.04-4.230.15712.679134230322990.09799.8
4.23-4.460.11514.818164221622050.07699.5
4.46-4.730.07618.138443209920920.06299.7
4.73-5.060.05920.578156198719840.05699.8
5.06-5.470.05520.667381181618080.05799.6
5.47-5.990.05521.366786170116950.0699.6
5.99-6.70.04323.465846153915300.05399.4
6.7-7.730.0327.274791135713490.04499.4
7.73-9.470.0232.994316115411510.03399.7
9.47-13.390.01736.0836449079030.03199.6
13.390.01735.9417965124560.03189.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
SHELXSphasing
RefinementMethod to determine structure: MIRAS / Resolution: 3.008→29.773 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7159 / SU ML: 0.94 / σ(F): 1.34 / Phase error: 34.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2948 1970 5.28 %Random
Rwork0.2633 ---
obs0.2649 37314 88.38 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.276 Å2 / ksol: 0.263 e/Å3
Displacement parametersBiso max: 233.07 Å2 / Biso mean: 106.6622 Å2 / Biso min: 50.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.1078 Å2-0 Å29.5691 Å2
2--5.6941 Å20 Å2
3----6.8018 Å2
Refinement stepCycle: LAST / Resolution: 3.008→29.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8489 0 10 0 8499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068658
X-RAY DIFFRACTIONf_angle_d1.00711793
X-RAY DIFFRACTIONf_chiral_restr0.0641420
X-RAY DIFFRACTIONf_plane_restr0.0051480
X-RAY DIFFRACTIONf_dihedral_angle_d15.0263107
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2144X-RAY DIFFRACTIONPOSITIONAL0.026
12B2144X-RAY DIFFRACTIONPOSITIONAL0.026
21C2019X-RAY DIFFRACTIONPOSITIONAL0.022
22D2019X-RAY DIFFRACTIONPOSITIONAL0.022
31C5X-RAY DIFFRACTIONPOSITIONAL0.024
32D5X-RAY DIFFRACTIONPOSITIONAL0.024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0077-3.08290.3896230.41734236512
3.0829-3.16610.5580.40631109116739
3.1661-3.25920.40821370.39662566270390
3.2592-3.36430.35561620.364428092971100
3.3643-3.48430.39091800.329428383018100
3.4843-3.62360.33261530.305828122965100
3.6236-3.78820.35581500.288328452995100
3.7882-3.98750.25991510.272728422993100
3.9875-4.23670.26321560.258728453001100
4.2367-4.56270.25711570.229428523009100
4.5627-5.01990.32061690.213228503019100
5.0199-5.74180.31031480.24228502998100
5.7418-7.2170.28471520.24372880303299
7.217-29.77450.22331740.22422904307899
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8382-0.02060.11066.0861-1.49222.6698-0.01660.33680.1307-0.7214-0.17270.64370.3050.15510.16580.64840.01680.14530.9575-0.22180.4354-23.5756-1.20319.0104
22.75060.36960.79222.29150.16214.36690.00750.44430.2304-0.6269-0.23770.5067-0.1004-0.63850.15371.250.0588-0.760.69790.03741.328-31.961927.797624.7336
30.923-0.42410.22032.43830.0310.85230.04370.1206-0.0082-0.11540.1024-0.13990.13880.1453-0.12831.0738-0.247-0.86250.0473-0.06861.3849-0.420621.384952.0282
44.04891.68130.17791.83941.2963.63120.03760.60360.2809-0.13850.427-0.44530.01350.6207-0.39230.83180.1075-0.34680.65640.02311.158514.12930.422827.3246
52.0001222.000122.00010.54755.24397.48899.8913-0.18695.50581.85119.0303-0.36220.75310.1376-0.03860.63930.09630.759-5.47697.641648.6972
62222220.65313.22388.32315.8875-0.21171.49652.80816.3052-0.44151.63310.11380.13521.60030.15711.700211.589214.208525.4946
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:326 )A4 - 326
2X-RAY DIFFRACTION2( CHAIN B AND RESID 4:326 )B4 - 326
3X-RAY DIFFRACTION3( CHAIN C AND RESID 5:266 )C5 - 266
4X-RAY DIFFRACTION4( CHAIN D AND RESID 10:266 )D10 - 266
5X-RAY DIFFRACTION5( CHAIN C AND RESID 301:301 )C301
6X-RAY DIFFRACTION6( CHAIN D AND RESID 301:301 )D301

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